This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Cryo-EM is emerging as a primary tool not only for the elucidation of structural information but also for the examination of dynamical properties of supramolecular assemblies. To complement emerging information from EM, it is tempting to use existing X-ray data to construct atomic models. As large assemblies often undergo large functional rearrangements, the conformations of the available X-ray structures may not correspond to the conformation apparent in the cryo-EM data. In such cases, the fitting can be rather complicated, since not only the correct orientation needs to be found but conformational rearrangements must also be considered. However, current approaches deform the molecule in an ad-hoc way. Therefore, we have introduced a novel method for the quantitative flexible docking of a high-resolution structure into low-resolution maps of macromolecular complexes from EM that takes into account the conformational flexibility of biological systems.